There's the scene where Rouge strangles Knuckles and yells at him for breaking the Master Emerald into pieces.
Rouge: What was that all about?! And LOOK WHAT YOU DID TO MY EMERALD!
Three words: Amy. Hugging. Shadow. The look on his face is priceless. And you thought Rouge was terrifying.
Sonic's delivery of the line "BLOWS UP?!"
Sonic Adventure 2, in the Dark Story before the Egg Golem boss. We get almost the same cutscene as when you fight it as Sonic, but in this version Sonic jumps up and delivers a kick to the golem which breaks the restraining mechanism on it and causes it to turn on Eggman. Though it's more of the dialogue that makes this hilarious:
Eggman: *When the Golem turns towards him* NOOOOOOOOOOO!
Made funnier by the fact that if you listen to it with the Japanese audio, it becomes "TEEEEEERIAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA!"
Omochao's reactions to getting hit can be pretty funny, especially when you weren't even the one who hit him and he still gets mad at you. Clearly, the programmers knew fans weren't gonna like him.
Basically, any moment when you're playing as Eggman, and take damage, sometimes he says "You! I'll make you pay for this!" He will say this when he takes damage from enemy attacks, running into enemies, even when he takes damage from a stage hazard, such as a spike, or a laser. What's funny there is the thought of him yelling at an inanimate object that didn't even intend to cause him any harm.
Sonic's second encounter with Shadow is supposed to be serious, but one simple error made it absolutely hilarious:
Sonic:I found you! Faker! Shadow: Faker? You're comparing yourself to the likes of me? Ha! I think YOU'RE the fake hedgehog around here! You're not even good enough to be my f- Sonic:I'LL MAKE YOU EAT THOSE WORDS!
Eggman catching the nightly news at his hideout.
"We interrupt this broadcawst for this impawtant news flawsh."
"Strangely, the only thing stolen was-" "A Chaos Emerald???" "-a Chaos Emerald."
"Eyewitnesses on the scene identified the culprit as world-renowned hero, Sonic the Hedgehog." (this said over a ridiculously high-quality shot of a black hedgehog with red eyes and white fur) "Looks more like the work ofShadow!"